Moving Cylinders into specific points
Poly Curves and Bevel Object

You could try to take advantage of curves instead of meshes.



This way you'll just have to control the cylinder main axis with two control points for each connection, you don't have to worry about the deformation because the cylinder is being built automatically and it's much easier to change the section size/shape.



To set up the curve like in the shown image sequence, choose a "Poly" Spline type once in edit mode and fill the Bevel Object field with the wanted section shape (in my case the little black bezier circle you can see near the origin).



Note: it's not your case, but if needed the cylinder ends can be capped by enabling the Fill Caps option in the Geometry panel of the Curve tab.